This application claims foreign priority benefits under Title 35, U.S.C., xc2xa7119(a)-(d) or xc2xa7365(a),(b) of foreign patent application no. GB 9908677.9, filed Apr. 15, 1999, the entire contents of which are incorporated herein by reference.
The invention relates to the field of genetic pharmacology and in particular to the screening of compounds for potential therapeutic activity using nematodes, principally but not exclusively, the nematode Caenorhabditis elegans. Specifically, the invention relates to the use of nematodes modified to have characteristics suitable for compound screening and to methods of selecting suitably modified nematodes from a population of nematodes.
Caenorhabditis elegans is a nematode worm which occurs naturally in the soil but can be grown easily in the laboratory on nutrient agar or in liquid nutrient broth inoculated with bacteria, preferably E. coli, on which it feeds. Each worm grows from an embryo to an adult worm of about 1 mm long in three days or so. As it is fully transparent at all stages in its life, cell divisions, migrations and differentiation can be seen in live animals. Furthermore, although its anatomy is simple its somatic cells represent most major differentiated tissue types including muscles, neurons, intestine and epidermis. Accordingly, differences in phenotype which represent a departure from that of a wild-type worm are relatively easily observed, either directly by microscopy or by using selective staining procedures. Many C. elegans mutants have been identified and their phenotype described, for example see C. elegans II Ed. Riddle, Blumenthal, Meyer and Priess, Cold Spring Harbor Laboratory Press, 1997.
Furthermore, standard methods are known for creating mutant worms with mutations in selected C. elegans genes, for example see J. Sutton and J. Hodgkin in xe2x80x9cThe Nematode Caenorhabditis elegansxe2x80x9d, Ed. by William B. Wood and the Community of C. elegans Researchers CSHL, 1988 594-595; Zwaal et al, xe2x80x9cTargetxe2x80x94Selected Gene Inactivation in Caenorhabditis elegans by using a Frozen Transposon Insertion Mutant Bankxe2x80x9d 1993, Proc. Natl. Acad. Sci. USA 90 pp 7431 -7435; Fire et al, Potent and Specific Genetic Interference by Double-Stranded RNA in C. elegans 1998, Nature 391, 860-811.
The C. elegans genome is now entirely sequenced and is available in a public database of t the Wellcome Trust Sanger Institute. As a result of the C. elegans genome sequencing project, it has emerged that C. elegans comprises genes which have equivalents that are widely distributed in most or all animals including humans.
The possibility that C. elegans might be useful for establishing interactions between external molecules and specific genes by comparison of C. elegans phenotypes which are generated by exposure to particular compounds and by selected mutations is considered by Rand and Johnson in Methods of Cell Biology, Chapter 8, volume 84, Caenorhabditis elegans: Modern Biological analysis of an Organism Ed. Epstein and Shakes, Academic Press, 1995 and J. Ahringer in Curr. Op. in Gen. and Dev. 7, 1997, 410-415.
Rand and Johnson in particular describe compound screening assays in which varying concentrations of the compound to be tested are added to nutrient agar or broth which is subsequently seeded with bacteria and then inoculated with worms. Any phenotypic changes in the worm as a result of exposure to the compound are then observed.
Although the nematode and in particular, C. elegans, is proving a powerful and efficient tool in the identification or discovery of pharmacologically active molecules, the presently known techniques for compound screening are not without drawbacks. A particular problem is that C. elegans, like higher organisms, is endowed with physiological barriers which prevent or minimise the ingress of foreign and potentially harmful substances. Because it normally lives in the dirt, this nematode has evolved a high number of pgp and mdr genes (Table 2) and hence has a high detoxification capacity which is a disadvantages for laboratory drug discovery purposes. In the past the only way in which these barriers have been overcome is to expose the worm to a high concentration of the compound to be tested, for example in the millimolar range. This is inconvenient because many of the compounds which might be screened in C. elegans are either only available in micromolar quantities or it is not economically feasible to use concentrations any higher than this. Furthermore, high concentrations of compounds may lead to death of the bacteria and hence starvation of the nematodes. It has also been observed that compounds crystallize when applied in high concentration.
If a compound is to reach a particular target in C. elegans it must overcome barriers in the pharynx, and in the gut and/or the cuticle. C. elegans feeds by taking in liquid containing its food (e.g. bacteria). It then spits out the liquid, crushes the food particles and internalises them into the gut lumen. This process is performed by the muscles of the pharynx. The process of taking up liquid and subsequently spitting it out is called pharyngeal pumping. Since this pumping process is stimulated to take place mainly in the presence of food, the pharynx is not pumping all the time in wild-type C. elegans. As a result, if worms are placed in a liquid culture in the presence of a dye a slow uptake and large variance in uptake amongst individual worms is observed.
Once a test compound has been internalised then the gut itself is a further frontier that may prevent the test compounds reaching their target site in the worm. This may be due to the presence of modifying and detoxifying enzymes in the gut, examples of which are the multi-drug resistance proteins (P-glycoproteins) and the multi-drug resistance related proteins.
Finally, C. elegans possesses a natural barrier to external substances which is the cuticle. The cuticle covers the outermost surfaces of the worm and also lines the pharynx and the rectum. It comprises mainly collagens and is substantially impermeable.
The present inventors have developed methods for compound screening in which the effect of these barriers to compound uptake is removed or diminished. These methods provide compounds assays of greater sensitivity while reducing the quantity of compound which must usually be used.
Therefore, in accordance with a first aspect of the invention there is provided a method of screening a compound for pharmacological activity which comprises observing a phenotypic change in a nematode when exposed to said compound in which said nematode exhibits constitutive pharyngeal pumping.
By xe2x80x9cconstitutive pharyngeal pumpingxe2x80x9d is meant constant pumping irrespective of the external or internal stimuli which would normally induce or repress such pumping.
The nematode may exhibit constitutive pharyngeal pumping as a result of a mutation in a relevant gene or alternatively may comprise a transgene which facilitates this phenotypic effect. Furthermore, the nematode may have other mutations or transgenes which result in the manifestation of another phenotypic characteristic which could be effected by the compound to be tested.
Caenorhabditis elegans is the most preferred nematode worm for use in the method of the invention. However, it will be appreciated that the method may also be carried out with other nematodes and in particular with other microscopic nematodes, preferably microscopic nematodes belonging to the genus Caenorhabditis. As used herein the term xe2x80x9cmicroscopicxe2x80x9d nematode encompasses nematodes of approximately the same size as C. elegans, being of the order 1 mm long in the adult stage. Microscopic nematodes of this approximate size are extremely suited for use in mid- to high-throughput screening as they can easily be grown in the wells of a multi-well plate of the type generally used in the art to perform such screening.
As aforesaid pharyngeal pumping is facilitated in C. elegans by the pharynx muscles and the contraction of these muscles is controlled by a set of neurons.
A list of the thirty-seven neurons and/or structural cells associated with the pharynx and pharyngeal pumping is shown in Table 4. A worm which exhibits an altered function in one or more of these neurons or cells which results in constitutive pharyngeal pumping is preferred for use in the method of the invention. In particular embodiments of the method, use of a worm exhibiting an altered function in one or more of the neurons, which according to C. elegans nomenclature are called MC, M3, M4 and NSM is preferred. These cells have been shown to control, respectively, the rate of pumping, timing of muscle relaxation, isthmus peristalsis and perception of food.
The main neurotransmitters involved in pharyngeal signalling have been identified as acetylcholine and serotonin, which are respectively functional in MC and NSM neurons. Other neurotransmitters such as glutamate, octopamine, dopamine, xcex3-aminobutyrate (GABA) and FMRF have also been shown to play a role in pumping. Accordingly, any mutant or transgenic worm which exhibits altered levels of one or more of these neurotransmitters may be suitable for use in the screening method of the invention. For example increased levels of serotonin are known to increase pharyngeal pumping.
As an alternative to using a worm which exhibits constitutive pharyngeal pumping, compound screening assays can be carried out in which a worm, wild-type in respect of pharyngeal pumping, is exposed both to the compound to be tested and a compound which induces or increases pharyngeal pumping. Such a compound for inducing or increasing pharyngeal pumping may be one of the neurotransmitters listed above or an agonist or antagonist of any one of these neurotransmitters, for example a serotonin agonist.
The benefit of using a worm in a compound screening assay which exhibits constitutive pharyngeal pumping, or has additional pharyngeal pumping induced, is that the worm will take up more medium into the gut as a function of time, independently of the presence of food in the medium. Furthermore, more of the compound which is dissolved in the medium will pass into the lumen of the gut. Thus, a higher concentration is available at that site to negotiate the gut barrier as discussed below. An additional advantage is that C. elegans populations with a constantly pumping pharynx grow more synchronously in the medium as their food uptake is more regular. This has the effect of simplifying the phenotypic observations which need to be made in a compound screen.
In accordance with a second aspect of the invention there is provided a method of screening a compound for potential pharmacological activity which comprises observing a phenotypic change in a nematode on exposure to said compound wherein said nematode exhibits increased gut permeability or increased uptake of foreign molecules through the gut wall. The nematode is preferably a microscopic nematode, as defined above, more preferably Caenorhabditis sp and may be a mutant or a transgenic worm comprising one or more mutations or transgenes which increase gut permeability or uptake and may also be responsible for the manifestation of another phenotypic characteristic associated with the target of the compound to be tested.
There are multiple factors which effect the uptake of compounds from the gut lumen to the surrounding tissues. These include the action of multi-drug resistance proteins (the P-glycoproteins) and the multi-drug resistance related proteins (MRPs) as well as other enzymes and mechanisms available for transport of molecules through the gut wall. Since test compounds will only reach the lumen of the gut through the pharynx it is preferable if worms which exhibit increased gut permeability or increased gut transport of foreign molecules also show constitutive pharyngeal pumping so that increased amounts of the test compound are both introduced into the gut lumen and transported into the surrounding tissues.
As an alternative to using a worm which exhibits increased gut permeability or increased gut transport of foreign molecules, compound screening assays may be performed in which a worm, wild-type in respect to gut permeability and uptake, is exposed to the compound to be tested and a compound which induces or increases the gut permeability or gut uptake. Such a compound may be a compound which inhibits or decreases the activity of multi-drug resistance proteins or multi-drug resistance related proteins or detoxification proteins. An example of these is cyclosporin A which inhibits the activity of multi-drug resistance proteins.
Worms, in particular microscopic nematodes such as C. elegans, which have been modified to increase the permeability of the outer cuticle are also useful for compound screening assays. Increased cuticle permeability may be a feature manifested in worms which also show constitutive pharyngeal pumping and increased gut permeability or increased gut uptake of foreign molecules. Worms with increased cuticle permeability may be transgenic or mutant worms obtained or created as aforesaid or alternatively they can be generated by treating the outer cuticle of the worms with a substance which induces cuticle permeability such as collagenase or bleach.
In one embodiment assays may be performed in which a wild-type worm is exposed to the compound to be tested and an enzyme or other suitable compound which creates or induces cuticle permeability.
It will be appreciated that worms having modifications such as those described above have significant advantages in compound screening assays since they are able to take up more compound, thereby increasing the sensitivity of the assay while reducing the amount of compound which must be used and hence the cost.
By xe2x80x9ccompoundxe2x80x9d is meant herein is any foreign molecule not usually present in the worm or to which the worm would not normally be exposed during its life cycle. For example, the worm may be exposed to a compound listed in a pharmacopoeia with known pharmacological activity. Alternatively, the compound may be one known to interact with a particular biochemical pathway or gene. A further alternative is to test known molecules with no known biological activity or completely new molecules or libraries of molecules such as might be generated by combinatorial chemistry. Compounds which are DNA, RNA, PNA, polypeptides or proteins are not excluded. Altered worm phenotypes which occur as a result of the compound exposure may be detected using light microscopy, differential interference contrast optics or fluorescence microscopy. In addition immuno-chemical detection, calorimetric detection or detection of fluorescence, luminescence or radioactive labels may be used. In some cases changed characteristics may be biochemical only and might be detected, for example by a change in pH in the growth media or a change in electrical potential. Different characteristics may need to be determined at different points in the growth cycle of the worm.
C. elegans mutants with the appropriate characteristics for increased compound intake as described above may be obtained from the C. elegans mutant collection at the C. elegans Genetic Center, University of Minnesota, St Paul, Minn., but may also be generated by standard methods. Such methods are described by Anderson in Methods in Cell Biology, Vol 48, xe2x80x9cC. elegans: Modern biological analysis of an organismxe2x80x9d Pages 31 to 58. Several selection rounds of the PCR technique can be performed to select a mutant worm with a deletion in a desired gene. Other methods of generating mutants with targeted defective gene expression are described by Sutton and Hodgkin, Zwaal et al and Fire et al as described above.
As aforesaid, for producing worms with enhanced uptake of compounds through the gut, particular genes which are targets to be mutated, deleted or otherwise knocked out are genes encoding multi-drug resistance proteins and multi-drug resistance related proteins.
In respect of generating mutant worms exhibiting constitutive pharyngeal pumping a target gene for modification is one encoding a protein involved in a pathway associated with the processing of one or more of the neurotransmitters acetylcholine, serotonin, glutamate, octopamine, dopamine, GABA or FMRF with a view to altering the levels thereof.
By xe2x80x9cprocessingxe2x80x9d is meant synthesis, transport, storage, release, re-uptake or degradation of the listed neurotransmitter.
As an alternative to mutation, transgenic worms may be generated with the appropriate characteristics. Methods of preparing transgenic worms are well known in the art and are particularly described by Craig Mello and Andrew Fire, Methods in Cell Biology, Vol 48, Ed. H. F. Epsein and D. C. Shakes, Academic Press, pages 452-480.
Following interventions to the worm to generate the relevant modifications to increase compound uptake as described above, it is necessary to be able to identify easily worms with the desired features and in particular those which exhibit the desired characteristics most strongly. Methods are available in the art for identification of mutant worms, such as those already listed. Alternatively, a genetic analysis may be used. However, a method which is specific for detecting worms with increased compound uptake is particularly desirable.
The present inventors have now developed a quicker and much more sensitive method to detect modified worms demonstrating the required degree of pharyngeal pumping and increased gut or cuticle permeability or compound uptake.
Thus, in accordance with a third aspect of the invention there is provided a method of identifying a mutant or transgenic nematode exhibiting increased uptake of compounds to be tested for potential pharmacological activity through the pharynx and/or gut and/or cuticle which comprises exposing said nematode to a compound incorporating a marker molecule which provides a detectable signal when taken up by the nematode and comparing the strength of said signal with the signal obtained from a wild-type worm when exposed to said marker molecule.
Preferably, the compound incorporating the marker molecule is one which only gives off its detectable signal once internalised in the worm, for example when cleaved by a worm enzyme or exposed to an environment found solely inside the worm.
In a particular embodiment the inventors have found that the fluorescent dye precursor calcein-AM available from Molecular Probes Europe BV, The Netherlands, is taken up through the pharynx by the worm and subsequently fluoresces, after cleavage of the AM moiety, in the gut lumen and/or in the surrounding cells if it passes the gut barrier. Worms which are able to take up more of the dye because of increased pharyngeal pumping fluoresce very brightly amongst a population of worms without that characteristic and therefore can be easily identified. Furthermore, the level of fluorescence can be quantified by methods known to those skilled in the art, thereby identifying those worms with the highest levels of pharyngeal pumping.
Because calcein fluoresces so brightly it is difficult to tell whether all of the fluorescent material remains in the gut lumen or whether any of it has passed to the surrounding cells and hence through the gut wall. In another embodiment the inventors have used a different fluorescent probe, BCECF-AM available from Molecular Probes (Europe BV), Netherlands. This dye only becomes fluorescent when cleaved by esterases and maintained at a pH above 6. The pH of the gut lumen is usually 5 or below. Thus, any BCECF-AM taken up through the pharynx into the gut lumen is not fluorescent until cleaved and the cleaved portion has entered the cells surrounding the lumen which are at a higher pH. Thus, this dye is able to quickly identify those mutants or otherwise modified worms which have increased gut transport or permeability. There is a gradual increase in fluoresence in the tissues surrounding the gut while the gut lumen remains dark. The fluorescence can be detected at an excitation wavelength of 485 nm and an emission wavelength of 530 nm.
Other compounds incorporating marker or signal generating molecules which will give a fluorescent signal include fluorescein diphosphate (FDP) and CMB-leu which are substrates of alkaline phosphate and endoproteases respectively.
As an alternative the marker molecule may be luminescent such as AMPPD or a glucorondiase substrate giving a coloured signal such as 5-bromo-4-chloro-3-indolyl glucuronic acid (X-gluc). All these compounds incorporating marker molecules may be obtained from molecular Probes Europe BV, The Netherlands.
A method of isolating mutant C. elegans strains which exhibit increased gut uptake (designated herein as gun mutant strains) using the marker dye BCECF-AM is described in the accompanying Examples. A specific gun mutant strain isolated using this procedure, strain bg85, was deposited on Dec. 23, 1999 in accordance with the provisions of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms in the Belgian Coordinated Collections of Microorganisms-BCCM LMBP- Collection, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000, Gent, Belgium under accession number LMBP 5334CB.
A C. elegans strain which exhibits constitutive pharyngeal pumping, designated strain HD8 or bg46 or hdr(bg46) see Example 1 below, was deposited on Feb. 9, 2000 in accordance with the provisions of the Budapest Treaty on the International Recognition of the Deposit of Microorganisms in the Belgian Coordinated Collections of Microorganisms-BCCM LMBP-Collection, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000, Gent, Belgium under accession number LMBP 5447CB.
In accordance with a fourth aspect of the invention there is provided a method of generating a C. elegans mutant exhibiting increased compound uptake which comprises:
Further characterization using the uptake assays described herein may be used to distinguish whether the increase of sensitivity is a general property due to increased compound uptake or is specific to the neurotransmitter in question.
In a particular embodiment the inventors have used the C. elegans mutant cha-1(cn101ts), which has a mutation in the gene encoding the choline acetyltransferase. A temperature sensitive mutation displays slow pumping, impaired movement and grows slowly. The effect can be rescued by exposing the worms to acetylcholine in the medium. This mutant can be grown on sub-rescuing amounts of acetylcholine, i.e. at a concentration that is only slightly lower than the rescuing concentration. Any additional mutation, induced by conventional mutagenesis as is state of the art, may increase the sensitivity of the cha-1 mutation to the acetylcholine that is in the medium in low concentration and thereby increase the growth rate considerably. In that way mutant worms sensitive to the neurotransmitter can be selected.
In a final aspect, the invention further provides for use of C. elegans strains with enhanced pharyngeal pumping, and/or enhanced gut uptake, and/or decreased drug metabolism, as described herein, in toxicity screening. In particular, the invention provides methods of testing compounds for potential toxicity which comprise observing a phenotypic change in a nematode when exposed to said compound wherein the gonematode exhibits enhanced or constitutive pharyngeal pumping, increased gut permeability or gut molecular transport or increased cuticle permeability.
Worms with increased permeability (i.e. defects in cuticle or gut barrier), increased pharynx pumping activity, or decreased ability to metabolise or to remove xenobiotics from the intracellular compartment into the gut lumen, relative to wild-type worms, would display a greater sensitivity to toxic compounds in general. Such worms designated as xe2x80x9csensitisedxe2x80x9d worms could be used to screen compounds for toxicity.
For the avoidance of doubt, where particular characteristics or properties of nematode worms are described herein by relative terms such as xe2x80x9cenhancedxe2x80x9d or xe2x80x9cincreasedxe2x80x9d or xe2x80x9cdecreasedxe2x80x9d this should be taken to mean enhanced, increased or decreased relative to wild-type nematodes. In the case of C. elegans, wild-type is defined as the N2 strain which is obtainable from the C. elegans Genetic Center, University of Minnesota, St Paul, Minn., USA.
Wild type nematodes in their natural environment live in close contact with xenobiotics synthesised and/or secreted by fungi, bacteria and plants in the soil and for that reason display high ability to prevent a broad range of potentially toxic compounds of diverse chemical structures from entering the internal compartment of the worm body. Thus by a creating a knock-out of these mechanisms of broad protection (structurally speaking), it is possible to open the internal compartment of the worm body (where the molecular targets of the toxin reside) to a wide range of chemical structures.
In the course of the drug discovery process, compounds selected after in vitro pharmacological screening are usually submitted to a wide range of secondary assays. These assays are aimed not only at measuring pharmacokinetic parameters but also at (1) assessing their pharmacological specificity, and (2) verifying the lack of toxicity. These tests are usually in vitro cytotoxicity assays where cell viability is monitored, or more precise measurements of specific mechanisms related to cell viability such as apoptosis, necrosis, DNA synthesis, protein synthesis, free radical production or redox level are made. Sensitised worms may be used as multicellular living models, to test the wide range of active compounds issued from the primary screening for any kind of toxicity, either of metabolic or pharmacological origin. Moreover, the phenotype produced by the toxic compounds could be linked to specific metabolic or pharmacologic pathways, thus giving insights to the mechanism of toxicity.
Caenorhabditis elegans is the preferred nematode worm for use in the toxicity testing methods of the invention. However, it will be appreciated that toxicity testing may also be carried out with other nematodes and in particular with other microscopic nematodes, preferably microscopic nematodes belonging to the genus Caenorhabditis. As used herein the term xe2x80x9cmicroscopicxe2x80x9d nematode encompasses nematodes of approximately the same size as C. elegans, being of the order 1 mm long in the adult stage. Microscopic nematodes of this approximate size are extremely suited for use in mid- to high-throughput screening as they can easily be grown in the wells of a multi-well plate of the type generally used in the art to perform such screening.
The nematodes will preferably be mutant or transgenic worms which display the desired characteristics of, for example, enhanced or constitutive pharyngeal pumping, increased gut permeability etc. Specific examples of such mutant and transgenic worms described hereinbefore, e.g. for use in compound screening, are also useful for toxicity testing.
For toxicity testing purposes, the compound under test will preferably be tested at a concentration from 0.1-100 xcexcM. Typically, the compound will be tested at a number of different concentrations within this range, with a preferred range of 1-10 xcexcM.
The read-out or end-point of a toxicity assay may be growth arrest or lethality or it may be a specific phenotype which is associated with exposure of a nematode to a toxic compound. Phenotypes associated with exposure to toxic compounds may be established by exposing the nematode to a compound which has known toxic activity and recording changes in the phenotype of the worm. This phenotype may then be used as the end-point of a toxicity assay.